Background: Fibromyalgia syndrome (FMS) is a chronic condition that causes pain, stiffness, and tenderness in muscles, tendons, and joints. It is also characterized by disturbed sleep, fatigue, anxiety, depression, and disturbances in bowel function. Management of FMS is at present very challenging as it contains multiple etiological factors and psychological tendencies; though, a patient-centered approach is essential to deal with this problem. Objective: To compare the efficacy of repetitive transcranial magnetic stimulation (rTMS) and transcranial direct current stimulation (tDCS) in improving pain and related disabilities in patients with primary (1ry) FM. Patients and Methods: Thirty patients with 1ry FM, 18 to 50 years old were randomized into 2 groups. Group I included 15 patients, who received 8 sessions (2/week for 4 consecutive weeks) of high frequency rTMS (10 Hz frequency) and Group II included 15 patients received 8 daily sessions of anodal tDCS (2 mA for 20 minutes) applied over the left primary motor cortex (M1). Results: Pain visual analogue scale (VAS), the revised Fibromyalgia Impact Questionnaire (FIQR), tender point scale, and Hospital Anxiety and Depression Scale (HADS) showed a significant decrease between baseline and follow-up assessments for both groups. Moreover, a significant change in all assessment scales was observed post-treatment when compared between both groups with more significant improvement in the group that received rTMS. Conclusion: Both rTMS and anodal tDCS of the left primary motor cortex showed marked improvement in symptoms of pain, functional disabilities and psychological status in patients with 1ry fibromyalgia. Both neuromodulator techniques can be considered as promising alternatives therapeutic options in the management of pain and related disabilities in FM.